Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA171576 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5 M-bM-^@M-^S 2 M-NM-<g Cd g-1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids. Genomic DNA from two F2 progeny pools (low leaf Cd pool and high leaf Cd pool) of CS28181 x Col-0 was labelled and hybridized separately to the Affymetrix SNP-tiling array AtSNPtile. The signal intensity difference between the two pools for all probes were analyzed using R scripts that are available at http://ars.usda.gov/mwa/bsasnp .
2012-07-30 | E-GEOD-39679 | biostudies-arrayexpress
Project description:Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5 – 2 μg Cd g-1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids.
2012-07-31 | GSE39679 | GEO
Project description:Many Arabidopsis thaliana accession show sensitvity to the air pollutant ozone, including the accession Cvi-0 from the Cape Verde Islands. To understand and assist in genetic mapping of loci causing the ozone sensitvity of Cvi-0, transcript profiling was performed in Cvi-0, the tolerant Col-0, and a near isogenic line (Col-S) where ozone sensitivity was introgressesed from Cvi-0 to Col-0 through eight rounds of backcrossing.
2017-08-09 | GSE102363 | GEO
Project description:To identify genes of the guard cell transcriptome of Arabidopsis thaliana enriched guard cell samples were compared with total leaf tissue. Genes of the abscisic acid and humidity response of Arabidopsis thaliana guard cells were identified by treatment with ABA-Spray and low humidity.
2013-01-14 | GSE41054 | GEO
Project description:We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1).
2011-07-27 | GSE29037 | GEO
Project description:To identify genes of the guard cell transkriptome of Arabidopsis thaliana enriched guard cell samples were compared with total leaf tissue. Genes of the abscisic acid and humidity response of Arabidopsis thaliana guard cells were identified by treatment with ABA-Spray and low humidity. Ost1-2 and slac1-3 mutants were compared to their wildtype.
2013-06-04 | GSE38639 | GEO
Project description:Elucidating direct roles of natural variation in biological processes has been challenging due to the difficulty in dissecting the causal role of a gene in traits displaying continuous variation. The decision of a seed to germinate is an easily quantifiable binary choice, which makes it an ideal phenotype to assess the contribution of natural variation in adaptation of plants to begin their lifecycle under optimal conditions. seeds must integrate a complex array of environmental signals to begin their lifecycle under optimal conditions. Light availability is a crucial environmental stimulus that promotes germination in many small seed plant species including Arabidopsis thaliana. Upon perception of light by photoreceptors, phytohormones act as internal signals to coordinate germination but the karrikin (KAR) signalling pathway through the HTL/KAI2 receptor is thought to play a rudimentary role in Arabidopsis germination (REF). Here we show that the AtHTL/KAI2 pathway is required and sufficient to promote germination under low light conditions. Activation of the AtHTL/KAI2 receptor by nanomolar Karrikin2 (KAR2) concentrations or inactivation of SMAX1 bypass the light requirement for germination. By performing a screen of A. thaliana accessions that can germinate under low light conditions, we identified an accession from Afghanistan (Ara-1) which misexpressed AtKAI2/HTL and had a nearly identical transcriptional signature to the activation of AtKAI2 upon addition of KAR2 in the reference accession. Our data suggest that AtKAI2 is a central regulator of germination in natural Arabidopsis populations in response to light availability, to optimize germination timing in their ecological niche.
2021-09-01 | GSE161704 | GEO
Project description:Arabidopsis thaliana is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has therefore attracted increasing interest as an alternative plant model species that possesses high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still far from complete and, due to the low number of ESTs available, evidence for actual transcriptional activity is lacking for most genes. ESTs were generated from a non-normalized and a normalized library synthesized from RNA pooled from plant samples from different developmental stages and grown under abiotic stress conditions. The ESTs of Thellungiella was sequenced by 454 pyrosequencing method. More than 1 million sequence reads were assembled into 42,810 unigenes, approximately 50% of which could be functionally annotated. From this sequence information, we constructed a 44k Agilent oligonucleotide microarray. A comparison of same-species and cross-species hybridization results showed the superior performance of the newly designed array for Thellungiella samples. In addition, the array was validated in a cold acclimation experiment that used the appropriately adapted MapMan software for analysis and visualization. To examine the quality of the Thellungiella array and to assess whether hybridization results from a dedicated array are superior to cross-species hybridization using the Arabidopsis array from the same manufacturer, we performed reciprocal array hybridizations. In this experiment, RNA from the Yukon accession of Thellungiella and RNA from the Col-0 accession of Arabidopsis were both hybridized on the Agilent Thellungiella and Arabidopsis expression arrays. For both species, RNA was extracted from acclimated and non-acclimated plants from three independent biological replicates.
2013-11-19 | E-GEOD-42156 | biostudies-arrayexpress
Project description:RNA-SEQ of Arabidopsis thaliana leaf tissues under normal and low CO2
2014-05-23 | E-MTAB-4419 | biostudies-arrayexpress
Project description:Arabidopsis thaliana (accession- Columbia) is an important model plant. RNA-Seq based study of 36 libraries was carried out to explore transcriptional programs operating in different plant parts (seedling, rosette, root, inflorescence, flower, fruit silique, and seed) and developmental stages (2-leaf stage, 6-leaf stage, 12-leaf stage, senescence stage, dry mature and imbibed seed stage). For each tissue type and developmental stage, three individual plants were used as biological replicates.
2022-05-04 | E-MTAB-6422 | biostudies-arrayexpress